Contacts of the strand formed by residues 270 - 278 (chain D) in PDB entry 2PI8
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 270 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39D PHE* 3.7 28.7 - - + -
57D GLN* 5.6 0.8 + - - -
60D VAL* 3.7 9.5 - - - +
61D TYR* 3.1 30.5 - - - -
64D VAL* 4.8 7.0 - - + -
268D GLY 3.5 1.6 + - - -
269D THR* 1.3 74.5 - - - +
271D LEU* 1.3 67.2 + - - +
292D LEU* 4.4 4.7 - - + -
293D MSE 3.7 2.9 - - - -
294D VAL* 4.6 2.9 - - - -
333D LEU* 3.1 58.8 + - + +
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Residues in contact with LEU 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258D VAL* 3.9 21.1 - - + -
265D ILE* 4.3 10.3 - - + -
269D THR* 3.7 26.2 - - + +
270D THR* 1.3 81.5 - - - +
272D ILE* 1.3 59.7 + - - +
273D ALA 3.9 0.3 + - - -
291D ARG 3.6 1.6 - - - +
292D LEU* 3.5 4.1 - - - -
293D MSE 2.7 49.8 + - + +
295D ALA* 4.6 3.6 - - + +
307D PHE* 3.7 35.9 - - + -
330D VAL* 3.9 18.6 - - + -
331D TRP 3.8 2.0 - - - -
332D VAL* 3.8 21.5 - - + -
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Residues in contact with ILE 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D PRO* 5.2 2.0 - - + -
33D PRO* 4.7 1.1 - - + -
67D TRP* 3.6 31.0 - - + -
74D THR* 3.9 14.6 - - + -
77D MSE 4.0 5.8 - - + -
270D THR 4.3 0.6 - - - -
271D LEU* 1.3 71.5 - - - +
273D ALA* 1.3 61.3 + - - +
290D LEU* 3.7 30.1 - - + -
291D ARG 3.3 8.1 - - - +
292D LEU* 3.6 17.9 - - + +
330D VAL* 3.4 1.2 - - - -
331D TRP* 2.9 56.8 + - + +
333D LEU* 3.8 16.7 - - + +
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Residues in contact with ALA 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D PHE* 3.8 22.9 - - + -
271D LEU 3.9 0.4 + - - -
272D ILE* 1.3 77.1 - - - +
274D GLU* 1.3 62.6 + - - +
275D VAL* 3.4 4.4 + - + +
289D GLU 3.1 3.5 - - - +
290D LEU* 3.6 5.7 - - - +
291D ARG* 2.9 33.1 + - - +
293D MSE 3.8 18.2 - - + -
329D ARG 3.3 13.2 - - - +
330D VAL* 3.8 9.6 - - + -
331D TRP* 4.6 1.1 - - - -
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Residues in contact with GLU 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D GLN* 4.8 1.0 + - - -
28D ASP 4.5 6.7 - - - +
29D ALA* 4.5 6.7 - - - +
98D PHE* 4.4 1.4 - - - -
273D ALA* 1.3 70.7 - - - +
275D VAL* 1.3 63.6 + - - +
276D PRO* 3.3 9.4 - - - +
288D TYR* 3.4 27.5 - - + +
289D GLU 3.4 3.2 + - - -
290D LEU* 3.5 35.1 + - + +
328D GLY* 3.8 11.4 - - - -
329D ARG* 3.0 55.9 + - - +
331D TRP* 4.2 13.7 - - + -
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Residues in contact with VAL 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D PHE* 4.8 4.0 - - + -
273D ALA* 4.2 8.1 - - + +
274D GLU* 1.3 70.8 - - - +
276D PRO* 1.3 67.8 - - + +
288D TYR* 4.2 0.2 - - - -
289D GLU* 2.8 53.3 + - + +
291D ARG* 4.5 11.7 - - + -
293D MSE 3.8 29.6 - - + -
309D ILE* 3.7 28.5 - - + -
324D TYR* 3.5 28.3 - - + +
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Residues in contact with PRO 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D GLY* 4.7 1.8 - - - -
98D PHE* 4.3 8.5 - - + -
274D GLU 3.3 9.4 - - - +
275D VAL* 1.3 84.9 - - + +
277D LEU* 1.3 62.1 + - - +
278D LEU* 4.5 1.7 - - - +
284D PHE* 3.6 23.3 - - + -
287D GLN 3.9 1.6 - - - +
288D TYR* 3.7 14.8 - - + -
324D TYR* 2.9 31.7 + - + -
326D HIS* 3.7 24.5 - - + -
327D TYR 3.2 27.8 - - - +
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Residues in contact with LEU 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B ARG* 2.9 49.6 - - + +
70B ALA* 3.9 1.8 - - - -
275D VAL 3.4 1.3 + - - +
276D PRO* 1.3 73.0 - - - +
278D LEU* 1.3 63.8 + - - +
284D PHE* 3.3 18.7 - - - -
285D ASN* 3.1 25.1 + - - +
287D GLN* 3.0 37.4 + - + +
288D TYR 3.3 27.1 - - - +
289D GLU* 3.8 26.0 - - + +
324D TYR* 4.4 5.8 - - - +
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Residues in contact with LEU 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B ARG* 6.0 3.5 - - - +
276D PRO 4.8 0.7 - - - +
277D LEU* 1.3 79.5 - - - +
279D ASP* 1.3 74.7 + - - +
282D GLY* 3.8 7.9 - - - +
283D LYS 3.4 16.8 - - - +
284D PHE* 4.4 0.9 - - - +
285D ASN* 4.1 6.5 - - - +
320D ARG* 4.7 7.0 - - + +
323D TRP* 3.8 35.4 - - + -
324D TYR* 4.4 31.5 + - + +
326D HIS* 3.6 37.2 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il